surface_area_of_lipid
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==== Overall Average SA/Lipid ==== | ==== Overall Average SA/Lipid ==== | ||
- | (author: Xiaohong Zhuang) | + | (authors: Xiaohong Zhuang |
- | If you are looking for multi lipid system, go to bottom. | + | === Introduction === |
- | ** Note: ** The gnuplot assumes you have standard truetype fonts. If you are doing analysis on DT2. Add the following | + | This simple analysis is used to estimate the overall average surface area (SA) per lipid. If you are analyzing a single component membrane then this is equivalent |
- | < | + | Those at UMD should use the ZT1 path: **/ |
- | setenv GDFONTPATH | + | |
+ | Outside of UMD a sample script is given in the gzip file: {{ : | ||
- | 1. The brief instruction to obtain and plot SA/ | + | Example |
- | Example of analysis: {{ : | + | === Instructions === |
- | This scripts that you need to calculate single lipid surface area per lipid using the gzip file: {{ :area_1_lipid.gz |}} | + | 1. Copy the folder //area_1_lipid// from the path highlighted above to your directory has contains all dyn files. // |
- | DT2 path: | + | 1.1 **Update area2.scr**: Change the 100 in line 23 ('' |
- | **/ | + | |
- | 1. Copy the folder | + | 2. The next set of instructions assume that you are running commands from the command line in the // |
- | **1.1 Update the 100 (or 36 if using the *.gz file not DT2 files) in area2.scr (line 23) to your value for the # lipid per leaflet** | + | 2.1. '' |
- | 2. Go to the // | + | < |
+ | ./area2.scr | ||
- | 2.1. It is used to calculate the surface | + | # Convert times steps to ns (assume 2fs/time which is always the case), and calculate the accumutive average of area |
+ | awk ' | ||
- | in order to find the dyn that the system reaches equilibrium. The key steps of 1_run_area.scr file are shown below: | + | # Generate the data file for plotting |
+ | sed -n ' | ||
+ | </ | ||
- | # To make files executable | + | * area2.scr |
- | '' | + | * The '' |
- | '' | + | * the '' |
- | # Run '' | + | You will need to run the scr file with type the following on the command line: '' |
- | + | ||
- | '' | + | |
- | + | ||
- | # Convert times steps to ns (Assume 2fs/step), and calculate | + | |
- | < | + | |
- | + | ||
- | # Generate the data file with reduced the number of the data points (1/50 of original) for plotting in excel. | + | |
- | + | ||
- | # The purpose of the reduction of data points is to avoid Excel clash to loading larger data points. | + | |
- | < | + | |
After run **1_run_area.scr**, | After run **1_run_area.scr**, | ||
+ | 2.2. Generate the plot of area vs. time in order to estimate the time the system reaches equilibrium with respect to the SA/lipid. | ||
- | 2.2. Generate the plot of area vs. time in order to find the dyn that the system reaches equilibrium | + | 2.2.1. |
- | + | ||
- | 2.2.1. | + | |
{{: | {{: | ||
Figure 1. Example surface area per lipid plot | Figure 1. Example surface area per lipid plot | ||
- | 2.2.2. If you don’t use WinSCP,or if you are not comfortable with Gnuplot, you can also use Excel to plot //area_time_acc_excel.dat// in Excel. The example of the plot in Excel is attached. | + | It is recommended to adjust the GnuPlot script to adjust the axis scale to best represent your data. Using nano or vim as an editor of //2_sa.gnu// |
- | Based on the area plot, we can determine when (at which dyn) the system reaches equilibrium. | + | < |
- | The equilibrium dyn number is the dyn file number that your cumulative (or running) average surface area per lipid (sa/lip) (red data points in Fig.1) becomes constant for around 20-30ns (i.e 10-15 dyn, refer to note). Since the running average including the beginning high values,we will also determine equilibrium based on the area per lipid (blue data points in Fig.1) that fluctuate around the same center line). | + | # show margin |
+ | plot [0:100] [35:50] \ | ||
+ | ' | ||
+ | ' | ||
+ | </ | ||
- | e.g. For in Fig.1, | + | The ranges after the //plot// command can be adjusted for the time (in ns) and SA. The other lines can be adjusted |
+ | 2.2.2. You can also use Excel to plot // | ||
- | 3. Based on equilibrated dyn range on step 2, select the data points from equilibrated dyn to the end to calculate the block-average surface areas. | + | 2.3. Estimating time for equilibration. |
- | 3.1 In 3_cal_avg_std.scr, | + | |
- | < | + | |
- | The example states that you want to do the averages from the last 20 dyn*dcd files. Let's say you have 50 dyn*.dcd files, then the first 30 files are ignored. If each file had 2ns of data, then you are calculating | + | Based on the area plot, you can determine when (at which dyn) the system reaches equilibrium. |
+ | The equilibrium dyn number is the dyn file number that your cumulative (or running) average surface area per lipid (sa/lip) (red data points in Fig.1) becomes constant (i.e 10-15 dyn, refer to note). Since the running average including the beginning high values, we will also determine equilibrium based on the area per lipid (blue data points in Fig.1) that fluctuate around | ||
+ | For in Fig.1, the cumulative average area (red) indicate that system reach equlibrium at around 30ns, and the areas (blue) fluctuate around the same center line, so we use the data from 50-100ns (dyn 26-50) or 60-100ns(dyn 31-50) to calculate the average area/lip. You will need to do the same for your system. | ||
- | # This following command calculates the block average, the output file name (// | + | 3. Obtaining Statistics of SA/Lipid |
- | 3.2 Calculate | + | Based on equilibrated dyn range determined in Step 2.3, select the data points from equilibrated dyn to the end to calculate |
- | # Store the output file name (// | + | 3.1 '' |
- | < | + | |
- | area-block.exe < area-block.inp </ | + | |
- | Note: For //#define MAX_R 100000// | + | |
- | As you can see, the output average area data are saved in area_avg_std.dat. The result is given in average+- population standard deviation. | + | Update |
- | 4. Calculate averages, sample standard deviation, and standard error of block averages by command: '' | + | < |
- | The file // | + | |
+ | The example states that you want to do the averages from the last 20 dyn*dcd files. Let's say you have 50 dyn*.dcd files, then the first 30 files are ignored. If each file had 2ns of data, then you are calculating the average from 60-100ns. | ||
- | Note: | + | 3.2 Calculate |
- | The corresponding nanosecond are based on the " | + | |
- | For example, in the //dyn-2.inp// file, we see there a code line: " | + | |
- | # run stops when this step is reached" | + | |
- | + | ||
- | and another code line: < | + | |
- | So you multiple 2fs/ | + | |
- | ==== Get the equilibrium data (test) ==== | + | **Note: **For //#define MAX_R 1000000// |
- | (author: Yalun Yu, | + | As you can see, the output average area data are saved in // |
- | + | ||
- | < Email me if anything | + | |
- | This is a brief instruction to obtain the time range of equilibrium (and also the minimum block size can be used for standard error calculation). Based on these, calculation of SA/lipid and Ka is done automatically for your lipid only system. Run Xiao's // | + | 3.3 Standard Errors from Block Average |
- | + | ||
- | 1. Install Anaconda (https:// | + | |
- | a) Download the python3.7 version for Linux [I used the ' | + | |
- | and put the .sh installer in your home directory (or any other place you can access and execute it) on DT2. | + | |
- | b) make the .sh file an executable (chmod u+x $NameOfInstaller.sh) | + | |
- | c) Install by running " | + | |
- | + | ||
- | 2. Make sure the Anaconda installation path is included (see below) in your ~/ | + | |
- | + | ||
- | In ~/ | + | |
- | set path = ($HOME/ | + | |
- | or in ~/ | + | |
- | | + | |
- | + | ||
- | 3. create a conda environment and activate the env. (see conda' | + | |
- | + | ||
- | 4. Install the pymbar package. | + | |
- | conda install -c omnia pymbar | + | |
- | + | ||
- | Download the script: {{ : | + | |
- | + | ||
- | Change the temperature and number of lipids per leaflet in // | + | |
- | set temp=323.15 | + | |
- | set nlip=36 | + | |
- | + | ||
- | Change the initial guess (or your preference) for block size (in ns) and the steps size (in ns) of your output (usually 1ps, but make sure to match your xst freq): | + | |
- | area_handling.py 10 0.001 >& all.dat | + | |
- | + | ||
- | After running // | + | |
+ | Calculate averages, sample standard deviation, and standard error of block averages by command: '' | ||
+ | The file // | ||
surface_area_of_lipid.1590628702.txt.gz · Last modified: 2020/05/27 21:18 by edit